Transcriptome analysis reveals potential mechanisms and pathways underlying embryonic development with respect to muscle growth and egg production in slow and fast growing chickens

Background: Chicken is one of the important meat sources throughout the globe. Muscle development and egg production are important genetic traits in commercially raising chickens. However, not much information is available in the fast and slow growth of chicken to determine the expression of genes involved in muscle development and egg production in embryo initiation and developmental stages. This study was designed to investigate why improved Aseel (PD4) growing slowly compared with the control broiler (CB), microarray was conducted with the 7 th -day embryo and 18 th -day thigh muscle of improved Aseel (PD4) and control broiler (CL), respectively. Results: : In the differential transcripts screening, all the transcripts obtained by microarray of slow and fast growth groups were screened by fold change ≥1 and false discovery rate (FDR) <0.05. In total, 19022 transcripts were differentially expressed between the 7 th -day embryo and 18 th -day thigh muscle of improved Aseel compared to the control broiler. Further analysis showed that a high number of transcripts are differentially regulated in the 7 th -day improved Aseel embryo (15382) and fewer transcripts were differentially regulated (3640) in the 18 th -day thigh muscle of improved Aseel compared to control broiler. In the 7 th and 18 th -day improved Aseel embryo, 10127, 2102, 5255, and 1538 transcripts were up and down-regulated, respectively. The commonly up and down-regulated transcripts are 545 and 381 between the 7 th and 18 th -day of embryos. In this study, we have selected 18 Gallus gallus candidate reference genes from NCBI and total RNA was isolated from control broiler, improved Aseel embryo tissues, and studied their expression profiles by real-time quantitative PCR (qPCR). The best housekeeping gene was identified by using geNorm, NormFinder, BestKeeper, Delta CT, and RefFinder analytical software. The result showed that the TFRC gene is the most stable and further it is used for qPCR data normalization. Further, to validate the differentially expressed genes (DEGs) related to muscle growth, myostatin signaling and development, fatty acid metabolism genes in improved Aseel (PD4) and control broiler embryo tissues by qPCR. Conclusion: Our study identified DEGs that regulate myostatin signaling and differentiation pathway, glycolysis and gluconeogenesis, fatty acid metabolism, Jak-STAT, mTOR, and TGF-β signaling pathways, tryptophan metabolism, PI3K-Akt signaling pathways in improved Aseel. The results revealed that the gene expression architecture is present in the improved Aseel exhibiting embryo growth that will help to improve muscle development, differentiation, egg production, as well as protein synthesis in improved Aseel native chicken. Our findings may be used as a model for improving the growth in improved Aseel as well as optimizing the growth in the control broiler.